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Home >> Genetics Dictionary >> Angiosperm genomes - Plant phylogeny
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Angiosperm genomes (plant phylogeny)
DNA C -value (the amount of deoxyribonucleic acid contained in the nuclei of unreplicated haploid cells or gametes) varies over several orders of magnitude among both higher plants and animals.
Genome size in angiosperms varies about 600fold from approximately 0.15 picogram of DNA for several species, for example, 0.16 pg [157 megabasepairs (Mbp)) in Arabidopsis thaliana, thale cress (n = 5 chromosomes) to nearly 90 pg (~ 88,000 Mbp) in Fritillaria davisii, a member of the lily family (n = 12 chromosomes).
(Part of the range of DNA content in plants, in which the very small chromosomes of an Arabidopsis relative, Crucihimalaya himalaica, are juxtaposed with the large chromosomes of loblolly pine, which contain 65 times more DNA.)
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Fig. Chromosomes (upper left inset) of Crucihimalaya himalaica (2CDNA content = 0.65 Pg, 2n = 16 chromosomes) juxtaposed with chromosomes at the same magnification of Pinus taeda (2C DNA content = 42.54 pg, 2n = 24 chromosomes).

The developmental and evolutionary significance of the massive variation in genome size is a major enigma of evolutionary biology. The so-called DNA C-value paradox involves the lack of overall correlation between genome size and phylogenetic advancement, the common occurrence of DNA content variation of greater than two- to threefold among congeneric species (species belonging to the same genus) with the same or similar chromosome numbers, and the fact that only a small amount (often less than 1%) of the nuclear DNA has coding functions.
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However, the results of 40 years of research involving higher plants indicate that DNA amount may be of developmental and adaptive significance through its biophysical effects on basic cellular features.
Developmental and adaptive significance of DNA content
The roles of varying DNA content in plant development and evolution have often been trivialized and dismissed as primarily resulting from the accumulation of junk, or selfish (noncoding), DNA. However, research suggests that DNA may play an important role by influencing plant phenotype, rate of development, and life history strategies through biophysical effects of its mass on nuclei and cells.
Effect of nucleotype on phenotype
DNA content positively correlates with chromosome volume, nuclear volume, cell volume, mitotic cycle time, and duration of meiosis. Michael Bennett has named these biophysical effects of total DNA content the nucleotype. Plant development involves a complex interaction of genetics (genotype) and environment, giving rise to observable properties (phenotype); however, the range of phenotypic expression under genetic control is limited by the plant's nucleotype.
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Rate of development
Bennett presented the hypothesis that DNA content is causally correlated with the rate of plant development. He proposed that attributes allowing an annual species to differentiate rapidly in a time-limited environment require low DNA content.
Thus, plants with large genomes are restricted to a perennial life form due to the growth-rate-limiting results of slow mitotic cycle time and long duration of meiosis.
Life history strategies
Patterns of DNA content variation exist at global, geographical, and climatic scales. Temperate plant families generally have larger genomes and a greater range of genome sizes compared with families restricted to tropical regions.
Plants with small genomes occur in both temperate and tropical families, but large genomes are generally found in species that grow under cool temperatures.
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Philip Grime and colleagues found that in a British plant community herbaceous species, which undergo their main growth in the cool conditions of early spring, had larger nuclear DNA contents than species with growth occurring in the warmer late spring and summer.
They suggested that climatic selection may operate on genome size through a differential effect of temperature upon cell division and cell expansion, such that at low temperature cell expansion is inhibited less than division.
This theory holds that under cold conditions growth should favor expansion of larger cells with higher DNA amounts whereas, under warmer conditions growth should be dominated by more rapidly dividing cells with lower DNA content.
Correlations also exist between ecological adaptation and genome size.
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For example, the diploid perennial species of Microseris and Agoseris (Western North American composite species related to the dandelion) occupy cooler and more mesic (having a moderate water supply) habitats than do the annual species that are adapted to warmer, more xeric (having a low or inadequate water supply), time-limited habitats. The annuals possess genomes that are only 30-60% the size of those of the perennials.
A similar pattern is observed among populations of the annual M. douglasii, in which DNA amount varies over 20%. The higher DNA values are restricted to plants growing in more mesic sites, generally on well-developed soils. Sites with lower rainfall and/or poorly developed soils dry out more quickly than mesic sites and reduce the time available to complete the plant's life cycle. In these species, DNA amount may be subject to natural selection through its nucleotypic effects on cell size, mitotic cycle time, and the rate of development.
Repetitive DNA and plant genome evolution
The dynamics of genome size evolution are speculative. In current evolutionary theory, genetic differences among related species are viewed as resulting from evolutionary forces, for example, selection and/or genetic drift, acting on existing variability within populations. However, an analogous hypothesis maintaining that accumulation of small deletions or duplications is the primary factor in changing genome size is not supported by the distribution of DNA contents.
Genome size commonly ranges severalfold among congeneric species, but well-documented examples of intraspecific variation in genome size are rare; genome size is typically very constant within a species. Since there is apparently a lack of existing variation in DNA content within species on which evolutionary forces can act, a hypothesis invoking events that generate larger discontinuous quantitative changes seems more attractive. Such events, if occurring, may be relatively rare and triggered by hybridization, environmental stress, or genetic events that destabilize the genome.
For the most part, variation in genome size is not caused by reiteration of coding genes, but is due to differences in the amount of repetitive DNA. Repetition of sequences, tandemly arranged and/or dispersed throughout the genome, comprise the bulk of eukaryotic DNA. Clusters of tandemly repeated sequences consisting of short repeats as small as a few basepairs long (microsatellites or simple sequence repeats) are dispersed throughout the genome. Longer tandemly repeated sequences, typically about 150 bp to 400 bp, are often of1 around centromeres of chromosomes.
Genome growth via retrotransposon accumulation
A mechanism to generate dispersed repetitive DNA sequences involves the movement and accumulation of retrotransposons, mobile DNA sequences that can move from one genomic location to another by producing ribonucleic acid (RNA) I :s transcribed by reverse transcriptase into DNA that is t. inserted at a new site. Members of a retrotransposon family may be several kilobasepairs long and have copy numbers up to several hundred thousand. The large copy numbers t can be attained by retrotransposons indicate that their amplification is one of the forces leading to the growth of a genome.
Genome reduction via retrotransposon crossing-over
Evidence is accumulating that indicates reductions in genome size have been common evolutionary events. Recombination in homologous regions of loops resulting from pairing of retrotransposons located in the same chromatid may be one mechanism for reducing the size of genomes that he extensively accumulated retrotransposons (Fig. 2). Although: there is evidence from DNA sequencing that such recombination events involving retrotransposons may occur in plants, it is not known if they occur frequently enough facilitate rapid evolutionary reductions in genome size.
Genome size and angiosperm phylogeny
It has been proposed that plants may have a "one-way tic to genomic obesity" as a consequence of retrotransposon accumulation and polyploidy (having one or more extra sets of chromosomes). Initial evaluations of the genomic obesity hypothesis have recently been conducted by superimposing estimated ancestral genome sizes onto well-established phylogenies (branching diagrams of evolutionary history),1 cotton (Gossypium) and its closely related genera in the cotton tribe (Gossypieae) and of the angiosperms to determine whether genome size only increases over the course of evolution or whether both increases and decreases occur.
In the cotton tribe, DNA content among diploid species varies over about a sevenfold range. Based on comparison of well-supported phylogeny for cotton and its allies with I pattern of evolutionary history generated from an analysis of
Fig. DNA detection by intrachromosomal recombination between (a) paired homologous terminal repeats of a single retrotransposon and (b) paired retrotransposons located on the same chromosome.
| 1.Retrotransposon |
2.& 3. Terminal Repeat |
4. Recombination |
5. Deleted Fragment |
| 6. Looping of the chromosome allows pairing of homologous terminal repeats that flank the retrotransposon. Recombination occurs between the terminal repeats. |
7. In the recombinant chromosome the retrotransposon is deleted except for a single terminal repeat. |
| 1. & 2. Retrotransposon |
3. Recombination |
4. Recombinant Chromosome |
5. Deleted Fragement |
| 6. Looping of the chromosome allows two homologous retransposons located on the same chromosome to pair and undergo recombination |
7. The Recombinant chromosome carries a deletionof one retrotransposon and the region between the retrotransposons |
DNA content of living species and estimated ancestral genome sizes, it was inferred that both increases and decreases genome size occurred during the evolution of this tribe. It found that the frequency of reductions actually exceeds that of increases.
Recent advances in plant taxonomy by participants of I Angiosperm Phylogeny Group using molecular phylogenetic data, including DNA sequences, along with nonmolecular phylogenetic data, have resulted in a revised classification the angiosperms that reflects evolutionary relationships. This phylogenetic framework and the availability of a list (currently 3500) of angiosperm genome sizes in the Plant DNA C-value Database are leading to analyses of evolution of genome size in relationship to angiosperm evolution. From initial broadly based analyses, it appears that the ancestral genome size for angiosperms was relatively small (1.4 pg), with the trend for the growth of genomes during the divergence of angiosperms.
However, apparent decreases in genome size accompanying angiosperm phylogeny were also detected. Large genomes (35 pg) in monocots and eudicots are confined to taxa occupying derived positions within larger clades. As additional genome sizes are added to the Plant DNA C-value Database, a more detailed picture of angiosperm genome size evolution will certainly be produced. It appears that a dynamic model that includes both increases and decreases for genome size evolution in plants is emerging.
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